Background: Female sex workers (FSW) and men who have sex with men (MSM) are highly vulnerable to HIV infection, but this population can be particularly difficult to reach in Central America due to stigma and violence. We aimed to estimate the number of FSW and MSM in the city of San Salvador, El Salvador to better plan HIV prevention activities. There are no published estimates for these populations in El Salvador.Methods: We used the multiplier method among MSM and FSW in San Salvador in 2008 for the estimation. The first source of data was collected by distributing key chains to both MSM and FSW populations through local nongovernmental organizations (NGOs) that work with these groups. The second source of data was collected during the course of a behavioral surveillance survey (BSS) using respondent driven sampling. The proportion of respondents that produced the key chain or described it correctly was used as the multiplier.The distribution of key chains was done one month before the start of data collection for the BSS survey.Results: Before the study 400 FSW and 400 MSM received a key chain. Of the 663 FSW interviewed in the BSS survey, 39 had received the key chain for a total estimate of 5,797 (95% confidence interval, 4,253 - 7,277) FSW in San Salvador. Of the 624 MSM who participated in the BSS survey, 36 had received the key chain, resulting in a total estimate of 12,500 (95% confidence interval, 7,235 - 17,725) MSM in San Salvador. Conclusions: Linking multiplier methodologies for population estimation to surveys can provide valuable information at a low cost. These data are crucial for program planning for national AIDS programs and NGOs working with these populations and for HIV estimation exercises.